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- PDB-3nn8: Crystal structure of engineered antibody fragment based on 3D5 -

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Basic information

Entry
Database: PDB / ID: 3nn8
TitleCrystal structure of engineered antibody fragment based on 3D5
ComponentsEngineered scFv
KeywordsIMMUNE SYSTEM / beta barrel / antibody fragment / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLieberman, R.L. / Maynard, J.A. / Drury, J.E. / Pai, J. / Culver, J.A.
CitationJournal: To be Published
Title: Peptide-binding single chain Antibody fragment (SCFV) chaperones for protein co-crystallization
Authors: Pai, J. / Culver, J.A. / Drury, J.E. / Lieberman, R.L. / Maynard, J.A.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Mar 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_comp_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_comp_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Engineered scFv
B: Engineered scFv
C: Engineered scFv
D: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)108,5564
Polymers108,5564
Non-polymers00
Water00
1
A: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-14 kcal/mol
Surface area10340 Å2
MethodPISA
2
B: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area10430 Å2
MethodPISA
3
C: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area10390 Å2
MethodPISA
4
D: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.637, 266.637, 266.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERAA116 - 236135 - 255
21GLNGLNSERSERBB116 - 236135 - 255
12GLNGLNSERSERCC116 - 236135 - 255
22GLNGLNSERSERDD116 - 236135 - 255
13ASPASPSERSERAA1 - 1222 - 141
23ASPASPSERSERBB1 - 1222 - 141
14ASPASPGLYGLYCC1 - 1152 - 116
24ASPASPGLYGLYDD1 - 1152 - 116

NCS ensembles :
ID
1
2
3
4
DetailsThere are 4 biological units in the asymmetric unit (chains A & B, chains C & F, chains D & E, chains G & H)

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Components

#1: Antibody
Engineered scFv


Mass: 27139.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 5.6 / Number: 158332 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / D res high: 3.1 Å / D res low: 154.303 Å / Num. obs: 28384 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.819.9387.810.0430.0435.4
6.939.810010.0570.0575.5
5.666.9310010.0850.0855.6
4.95.6610010.0840.0845.6
4.384.910010.0820.0825.6
44.3810010.0880.0885.6
3.71410010.1370.1375.6
3.473.7110010.1780.1785.6
3.273.4710010.2240.2245.6
3.13.2710010.3420.3425.6
ReflectionResolution: 3.1→154.303 Å / Num. all: 28384 / Num. obs: 28384 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.275.60.3422.12295541340.342100
3.27-3.475.60.2243.22179738960.224100
3.47-3.715.60.17842064436810.178100
3.71-45.60.1375.21920834210.137100
4-4.385.60.0887.91777231730.088100
4.38-4.95.60.0828.51605728660.082100
4.9-5.665.60.0848.41409725240.084100
5.66-6.935.60.0858.31209921740.085100
6.93-9.85.50.05711.6926216850.057100
9.8-19.9285.40.04314.144418300.04387.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å19.88 Å
Translation3.19 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KTR

1ktr


Resolution: 3.1→154.3 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.2196 / WRfactor Rwork: 0.1673 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8443 / SU B: 33.974 / SU ML: 0.282 / SU R Cruickshank DPI: 0.321 / SU Rfree: 0.3905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1439 5.1 %RANDOM
Rwork0.1831 ---
obs0.1858 28371 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.15 Å2 / Biso mean: 69.6674 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: LAST / Resolution: 3.1→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 0 0 7272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227444
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.95910086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2685939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67323.649296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7431540
X-RAY DIFFRACTIONr_chiral_restr0.1090.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215584
X-RAY DIFFRACTIONr_mcbond_it0.4551.54675
X-RAY DIFFRACTIONr_mcangle_it0.9327524
X-RAY DIFFRACTIONr_scbond_it1.34432769
X-RAY DIFFRACTIONr_scangle_it2.2954.52562
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A938MEDIUM POSITIONAL0.260.5
1A938MEDIUM THERMAL0.312
2C938MEDIUM POSITIONAL0.270.5
2C938MEDIUM THERMAL0.312
3A874MEDIUM POSITIONAL0.420.5
3A874MEDIUM THERMAL0.372
4C883MEDIUM POSITIONAL0.490.5
4C883MEDIUM THERMAL0.392
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 99 -
Rwork0.251 1961 -
all-2060 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.78741.01531.78434.14921.46846.4684-0.03580.09040.23270.09960.0866-0.3080.0665-0.5396-0.05070.05690.02690.0110.08080.00250.1292-22.482-51.9011.147
24.7104-4.48180.23418.11560.92075.8984-0.3507-0.66960.07470.80450.23070.10120.0269-0.60250.120.18230.1314-0.0480.3591-0.09370.1596-33.515-41.2715.445
34.2158-0.68661.36196.6399-1.39567.3893-0.0056-0.0836-0.2449-0.05520.0283-0.3305-0.5278-0.0209-0.02270.0604-0.02440.01130.0376-0.0250.1459-51.882-110.8131.172
45.52130.90930.54676.5841-1.72526.242-0.1449-0.04070.23020.03570.1356-0.14850.4161-0.01710.00930.05860.0555-0.02570.1503-0.05270.0388-56.054-20.609-0.013
59.0767-6.0361-0.32068.1794-0.58574.12590.74221.2327-0.1172-0.9724-0.8427-0.09740.20220.00410.10050.36660.24280.05370.35270.05840.0707-44.293-29.897-14.574
68.89094.65730.60855.5146-0.54495.47650.2867-0.81420.11190.6468-0.4457-0.0767-0.60110.06550.15890.3454-0.1366-0.08020.23310.05910.1387-41.305-99.78615.454
77.32670.222-2.16175.3757-0.3026.35070.0512-0.1037-0.14250.0518-0.1829-0.29210.0916-0.48860.13170.1276-0.0581-0.03750.07290.01740.0292-20.615-77.244-0.032
88.03626.3314-1.44510.0422-0.08495.0103-0.85271.0771-0.1652-1.12370.81250.02840.0403-0.29310.04020.3103-0.23020.02220.3481-0.03510.0904-29.906-88.988-14.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 230
2X-RAY DIFFRACTION2A1 - 115
3X-RAY DIFFRACTION3B116 - 230
4X-RAY DIFFRACTION4C116 - 230
5X-RAY DIFFRACTION5C1 - 115
6X-RAY DIFFRACTION6B1 - 115
7X-RAY DIFFRACTION7D116 - 230
8X-RAY DIFFRACTION8D1 - 115

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